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diffexp_male_female.R
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diffexp_male_female.R
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setwd('/Users/onurdogan/Desktop/diffexp-results_analysis/Gaffney/')
library("writexl")
#diffexp analysis part
# male-female
male <- read.csv("DESeq2_ernest_male.csv")
female <- read.csv("DESeq2_ernest_female.txt")
rownames(male)=male$X
rownames(female)=female$X
cc_male_05<-male[which(male[,'padj']<0.05,),'X']
cc_female_05<-female[which(female[,'padj']<0.05,),'X']
diff_pval.05<-setdiff(cc_male_05,cc_female_05)
res_cc_male.05=male[diff_pval.05,c('X','log2FoldChange','padj')]
res_cc_female.05=female[diff_pval.05,c('log2FoldChange','padj')]
colnames(res_cc_male.05)=c("X","mcase_vs_mcontrol_LFC","mcase_vs_mcontrol_padj")
colnames(res_cc_female.05)=c("fcase_vs_fcontrol_LFC","fcase_vs_fcontrol_padj")
s=cbind(res_cc_male.05,res_cc_female.05)
write_xlsx(data.frame(s), "Gaffney-male_female-diff-0.05.xlsx")
#.1
cc_male_1<-male[which(male[,'padj']<0.1,),'X']
cc_female_1<-female[which(female[,'padj']<0.1,),'X']
diff_pval.1<-setdiff(cc_male_1,cc_female_1)
res_cc_male.1=male[diff_pval.1,c('X','log2FoldChange','padj')]
res_cc_female.1=female[diff_pval.1,c('log2FoldChange','padj')]
colnames(res_cc_male.1)=c("X","mcase_vs_mcontrol_LFC","mcase_vs_mcontrol_padj")
colnames(res_cc_female.1)=c("fcase_vs_fcontrol_LFC","fcase_vs_fcontrol_padj")
s2=cbind(res_cc_male.1,res_cc_female.1)
write_xlsx(data.frame(s2), "Gaffney-male_female-diff-0.1.xlsx")
# sign analysis part
male_05<-male[which(male[,'padj']<0.05,),'X']
female_05<-female[which(female[,'padj']<0.05,),'X']
intersect_05<-intersect(male_05,female_05)
a=male[intersect_05,c('X','log2FoldChange')]
b=female[intersect_05,c('X','log2FoldChange')]
for (i in intersect_05){
if(sign(a[i,'log2FoldChange'])!=sign(b[i,'log2FoldChange'])){
print(a[i,'X'])
}
}
male_1<-male[which(male[,'padj']<0.1,),'X']
female_1<-female[which(female[,'padj']<0.1,),'X']
intersect_1<-intersect(male_1,female_1)
a=male[intersect_1,c('X','log2FoldChange')]
b=female[intersect_1,c('X','log2FoldChange')]
for (i in intersect_1){
if(sign(a[i,'log2FoldChange'])!=sign(b[i,'log2FoldChange'])){
print(a[i,'X'])
}
}
#female-male
# male-female
cc_male_05<-male[which(male[,'padj']<0.05,),'X']
cc_female_05<-female[which(female[,'padj']<0.05,),'X']
diff_pval.05<-setdiff(cc_female_05,cc_male_05)
res_cc_male.05=male[diff_pval.05,c('log2FoldChange','padj')]
res_cc_female.05=female[diff_pval.05,c('X','log2FoldChange','padj')]
colnames(res_cc_male.05)=c("mcase_vs_mcontrol_LFC","mcase_vs_mcontrol_padj")
colnames(res_cc_female.05)=c("X","fcase_vs_fcontrol_LFC","fcase_vs_fcontrol_padj")
s=cbind(res_cc_female.05,res_cc_male.05)
write_xlsx(data.frame(s), "Gaffney-female_male-diff-0.05.xlsx")
#.1
cc_male_1<-male[which(male[,'padj']<0.1,),'X']
cc_female_1<-female[which(female[,'padj']<0.1,),'X']
diff_pval.1<-setdiff(cc_female_1,cc_male_1)
res_cc_male.1=male[diff_pval.1,c('log2FoldChange','padj')]
res_cc_female.1=female[diff_pval.1,c('X','log2FoldChange','padj')]
colnames(res_cc_male.1)=c("mcase_vs_mcontrol_LFC","mcase_vs_mcontrol_padj")
colnames(res_cc_female.1)=c("X","fcase_vs_fcontrol_LFC","fcase_vs_fcontrol_padj")
s2=cbind(res_cc_female.1,res_cc_male.1)
write_xlsx(data.frame(s2), "Gaffney-female_male-diff-0.1.xlsx")
# sign analysis part
male_05<-male[which(male[,'padj']<0.05,),'X']
female_05<-female[which(female[,'padj']<0.05,),'X']
intersect_05<-intersect(female_05,male_05)
a=male[intersect_05,c('X','log2FoldChange')]
b=female[intersect_05,c('X','log2FoldChange')]
for (i in intersect_05){
if(sign(a[i,'log2FoldChange'])!=sign(b[i,'log2FoldChange'])){
print(b[i,'X'])
}
}
male_1<-male[which(male[,'padj']<0.1,),'X']
female_1<-female[which(female[,'padj']<0.1,),'X']
intersect_1<-intersect(female_1,male_1)
a=male[intersect_1,c('X','log2FoldChange')]
b=female[intersect_1,c('X','log2FoldChange')]
for (i in intersect_1){
if(sign(a[i,'log2FoldChange'])!=sign(b[i,'log2FoldChange'])){
print(b[i,'X'])
}
}